TiddlyWiki is quite a famous note-taking system. Describing itself as “a non-linear personal web notebook”, it’s actually quite a bit more than that. Thanks to a plugin system, it’s basically an app platform, and plenty of cool stuff has been made for it.
And it exists as a unique thing: a self-contained web application—a single HTML file with both the app and the content—that you can take around on a USB flash drive. Oh wait… who even uses those anymore for anything other than OS installers and bringing files to a print shop?